10 20 30 40 50 60 70 80 4PTD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 18-JUL-97 4PTD
TITLE PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C MUTANT D274N
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PI-PLC; COMPND 5 EC: 3.1.4.10; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 CELLULAR_LOCATION: SECRETED INTO MEDIUM; SOURCE 5 GENE: PI-PLC GENE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MM294; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: PERIPLASM; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBR322 RELATED; SOURCE 12 EXPRESSION_SYSTEM_GENE: PI-PLC D198E GENE; SOURCE 13 OTHER_DETAILS: GENE CLONED IN ESCHERICHIA COLI
KEYWDS HYDROLASE, PHOSPHORIC DIESTER, LIPID DEGRADATION, KEYWDS 2 PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C
EXPDTA X-RAY DIFFRACTION
AUTHOR D.W.HEINZ
REVDAT 2 24-FEB-09 4PTD 1 VERSN REVDAT 1 21-JAN-98 4PTD 0
JRNL AUTH C.S.GASSLER,M.RYAN,T.LIU,O.H.GRIFFITH,D.W.HEINZ JRNL TITL PROBING THE ROLES OF ACTIVE SITE RESIDUES IN JRNL TITL 2 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM JRNL TITL 3 BACILLUS CEREUS BY SITE-DIRECTED MUTAGENESIS. JRNL REF BIOCHEMISTRY V. 36 12802 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9335537 JRNL DOI 10.1021/BI971102D
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.W.HEINZ,M.RYAN,T.L.BULLOCK,O.H.GRIFFITH REMARK 1 TITL CRYSTAL STRUCTURE OF THE REMARK 1 TITL 2 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM REMARK 1 TITL 3 BACILLUS CEREUS IN COMPLEX WITH MYO-INOSITOL REMARK 1 REF EMBO J. V. 14 3855 1995 REMARK 1 REFN ISSN 0261-4189
REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0001 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.6 REMARK 3 NUMBER OF REFLECTIONS : 12216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 584 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1312 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.66 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.049 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2422 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.39 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.21 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 4PTD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XENTRONICS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13525 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 6.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 200 DATA REDUNDANCY : 1.570 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.16400 REMARK 200 R SYM FOR SHELL (I) : 0.18200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: WILD-TYPE PI-PLC REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.35000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.30000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 297 REMARK 465 GLU A 298
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 12 30.55 -142.50 REMARK 500 ASP A 75 1.61 -65.60 REMARK 500 TYR A 88 48.16 -74.09 REMARK 500 GLU A 146 -168.96 -124.91 REMARK 500 TYR A 177 -74.71 -21.75 REMARK 500 TRP A 178 76.19 54.95 REMARK 500 ASN A 181 70.93 48.05 REMARK 500 ASN A 189 -156.49 -137.33 REMARK 500 ASN A 221 33.71 -99.25 REMARK 500 THR A 240 9.99 56.50 REMARK 500 ALA A 241 76.45 -176.00 REMARK 500 TRP A 242 26.29 49.78 REMARK 500 TYR A 275 73.09 39.07 REMARK 500 ASN A 277 -156.07 -157.01 REMARK 500 LEU A 283 89.29 78.67 REMARK 500 ALA A 291 2.18 -69.63 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 313 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 326 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH A 339 DISTANCE = 5.48 ANGSTROMS REMARK 525 HOH A 356 DISTANCE = 5.01 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE.
DBREF 4PTD A 1 298 UNP P14262 PLC_BACCE 32 329
SEQADV 4PTD ASN A 274 UNP P14262 ASP 305 ENGINEERED
SEQRES 1 A 298 ALA SER SER VAL ASN GLU LEU GLU ASN TRP SER LYS TRP SEQRES 2 A 298 MET GLN PRO ILE PRO ASP SER ILE PRO LEU ALA ARG ILE SEQRES 3 A 298 SER ILE PRO GLY THR HIS ASP SER GLY THR PHE LYS LEU SEQRES 4 A 298 GLN ASN PRO ILE LYS GLN VAL TRP GLY MET THR GLN GLU SEQRES 5 A 298 TYR ASP PHE ARG TYR GLN MET ASP HIS GLY ALA ARG ILE SEQRES 6 A 298 PHE ASP ILE ARG GLY ARG LEU THR ASP ASP ASN THR ILE SEQRES 7 A 298 VAL LEU HIS HIS GLY PRO LEU TYR LEU TYR VAL THR LEU SEQRES 8 A 298 HIS GLU PHE ILE ASN GLU ALA LYS GLN PHE LEU LYS ASP SEQRES 9 A 298 ASN PRO SER GLU THR ILE ILE MET SER LEU LYS LYS GLU SEQRES 10 A 298 TYR GLU ASP MET LYS GLY ALA GLU ASP SER PHE SER SER SEQRES 11 A 298 THR PHE GLU LYS LYS TYR PHE VAL ASP PRO ILE PHE LEU SEQRES 12 A 298 LYS THR GLU GLY ASN ILE LYS LEU GLY ASP ALA ARG GLY SEQRES 13 A 298 LYS ILE VAL LEU LEU LYS ARG TYR SER GLY SER ASN GLU SEQRES 14 A 298 PRO GLY GLY TYR ASN ASN PHE TYR TRP PRO ASP ASN GLU SEQRES 15 A 298 THR PHE THR THR THR VAL ASN GLN ASN ALA ASN VAL THR SEQRES 16 A 298 VAL GLN ASP LYS TYR LYS VAL SER TYR ASP GLU LYS VAL SEQRES 17 A 298 LYS SER ILE LYS ASP THR MET ASP GLU THR MET ASN ASN SEQRES 18 A 298 SER GLU ASP LEU ASN HIS LEU TYR ILE ASN PHE THR SER SEQRES 19 A 298 LEU SER SER GLY GLY THR ALA TRP ASN SER PRO TYR TYR SEQRES 20 A 298 TYR ALA SER TYR ILE ASN PRO GLU ILE ALA ASN TYR ILE SEQRES 21 A 298 LYS GLN LYS ASN PRO ALA ARG VAL GLY TRP VAL ILE GLN SEQRES 22 A 298 ASN TYR ILE ASN GLU LYS TRP SER PRO LEU LEU TYR GLN SEQRES 23 A 298 GLU VAL ILE ARG ALA ASN LYS SER LEU ILE LYS GLU
FORMUL 2 HOH *60(H2 O)
HELIX 1 1 VAL A 4 GLU A 8 5 5 HELIX 2 2 SER A 34 LYS A 38 5 5 HELIX 3 3 PRO A 42 TRP A 47 1 6 HELIX 4 4 PHE A 55 HIS A 61 1 7 HELIX 5 5 LEU A 91 ASP A 104 1 14 HELIX 6 6 PHE A 128 LYS A 135 1 8 HELIX 7 7 LEU A 151 ALA A 154 1 4 HELIX 8 8 TYR A 204 ASN A 220 1 17 HELIX 9 9 PRO A 245 LYS A 263 1 19 HELIX 10 10 LEU A 284 ASN A 292 1 9
SHEET 1 A 5 ILE A 28 THR A 31 0 SHEET 2 A 5 TRP A 270 GLN A 273 1 N VAL A 271 O ILE A 28 SHEET 3 A 5 HIS A 227 PHE A 232 1 N ASN A 231 O TRP A 270 SHEET 4 A 5 ASN A 193 ASP A 198 1 N ASN A 193 O LEU A 228 SHEET 5 A 5 GLU A 182 THR A 187 -1 N THR A 186 O VAL A 194 SHEET 1 B 4 ILE A 78 LEU A 80 0 SHEET 2 B 4 ILE A 65 LEU A 72 -1 N ARG A 71 O VAL A 79 SHEET 3 B 4 ILE A 110 LYS A 116 1 N ILE A 111 O PHE A 66 SHEET 4 B 4 ILE A 158 ARG A 163 1 N VAL A 159 O ILE A 110
SITE 1 ACT 2 HIS A 32 HIS A 82
CRYST1 44.700 44.600 153.300 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.022371 0.000000 0.000000 0.00000
SCALE2 0.000000 0.022422 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006523 0.00000